SoroushVahidi/scidocs huggingface dataset:
Extraction and classification texture of inflammatory cells and nuclei in normal pap smear images
(2015)

The presence of inflammatory cells complicates the process of identifying the nuclei in the early detection of cervical cancer. Inflammatory cells need to be eliminated to assist pathologists in reading Pap smear slides. The texture of Grey-Level Run-Length Matrix (GLRLM) for inflammatory cells and nuclei types are investigated. The inflammatory cells and nuclei have different texture, and it can be used to differentiate them. To extract all of the features, firstly manual cropping of inflammatory cells and nuclei needs to be done. All of extracted features have been analyzed and selected by Decision Tree classifier (J48). Originally there have been eleven features in the direction of 135° which are extracted to classify cropping cells into inflammatory cells and nuclei. Then the eleven features are reduced into eight, namely low gray level run emphasis, gray level non uniformity, run length non-uniformity, long run low gray-level emphasis, short run high gray-level emphasis, short run low gray-level emphasis, long run high gray-level emphasis and run percentage based on the rule of classification. This experiment is applied into 957 cells which were from 50 images. The compositions of these cells were 122 cells of nuclei and 837 cells of inflammatory. The proposed algorithm applied to all of the cells and the result of classification by using these eight texture features obtains the sensitivity rates which show that there are still nuclei of cells that were considered as inflammatory cells. It was in accordance with the conditions of the difficulties faced by the pathologist while the specificity rate suggests that inflammatory cells detected properly and few inflammatory cells are considered as nucleus.
Development of Autonomous Car—Part II: A Case Study on the Implementation of an Autonomous Driving System Based on Distributed Architecture
(2015)

Part I of this paper proposed a development process and a system platform for the development of autonomous cars based on a distributed system architecture. The proposed development methodology enabled the design and development of an autonomous car with benefits such as a reduction in computational complexity, fault-tolerant characteristics, and system modularity. In this paper (Part II), a case study of the proposed development methodology is addressed by showing the implementation process of an autonomous driving system. In order to describe the implementation process intuitively, core autonomous driving algorithms (localization, perception, planning, vehicle control, and system management) are briefly introduced and applied to the implementation of an autonomous driving system. We are able to examine the advantages of a distributed system architecture and the proposed development process by conducting a case study on the autonomous system implementation. The validity of the proposed methodology is proved through the autonomous car A1 that won the 2012 Autonomous Vehicle Competition in Korea with all missions completed.
Digital Image Processing
(1981)

Image defects which could be caused by the digitization process or by faults in the imaging set-up (for example, bad lighting) can be corrected using Image Enhancement techniques. Once the image is in good condition, the Measurement Extraction operations can be used to obtain useful information from the image. Course Objectives “Introduction to Digital Image Processing” is two-day hands-on course that provide fundamental concepts and techniques for digital image processing and the software principles used in their practical implementation.
Python for Prototyping Computer Vision Applications
(2010)

Python is a popular language widely adopted by the scientific community due to its clear syntax and an extensive number of specialized packages. For image processing or computer vision development, two libraries are prominently used: NumPy/SciPy and OpenCV with a Python wrapper. In this paper, we present a comparative evaluation of both libraries, assessing their performance and their usability. We also investigate the performance of OpenCV when accessed through a python wrapper versus directly using the native C implementation.
Image Alignment and Stitching : A Tutorial 1
(2004)

This tutorial reviews image alignment and image stitching algorithms. Image alignment algorithms can discover the correspondence relationships among images with varying degrees of overlap. They are ideally suited for applications such as video stabilization, summarization, and the creation of panoramic mosaics. Image stitching algorithms take the alignment estimates produced by such registration algorithms and blend the images in a seamless manner, taking care to deal with potential problems such as blurring or ghosting caused by parallax and scene movement as well as varying image exposures. This tutorial reviews the basic motion models underlying alignment and stitching algorithms, describes effective direct (pixel-based) and feature-based alignment algorithms, and describes blending algorithms used to produce seamless mosaics. It closes with a discussion of open research problems in the area.
Substrate-Independent Microwave Components in Substrate Integrated Waveguide Technology for High-Performance Smart Surfaces
(2018)

Although all existing air-filled substrate integrated waveguide (AFSIW) topologies yield a substrate-independent electrical performance, they rely on dedicated, expensive, laminates to form air-filled regions that contain the electromagnetic fields. This paper proposes a novel substrate-independent AFSIW manufacturing technology, enabling straightforward integration of high-performance microwave components into a wide range of general-purpose commercially available surface materials by means of standard additive (3-D printing) or subtractive (computer numerically controlled milling/laser cutting) manufacturing processes. First, an analytical formula is derived for the effective permittivity and loss tangent of the AFSIW waveguide. This allows the designer to reduce substrate losses to levels typically encountered in high-frequency laminates. Then, several microwave components are designed and fabricated. Measurements of multiple AFSIW waveguides and a four-way power divider/combiner, both relying on a new coaxial-to-air-filled SIW transition, prove that this novel approach yields microwave components suitable for direct integration into everyday surfaces, with low insertion loss, and excellent matching and isolation over the entire [5.15–5.85] GHz band. Hence, this innovative approach paves the way for a new generation of cost-effective, high-performance, and invisibly integrated smart surface systems that efficiently exploit the area and the materials available in everyday objects.
VIPS: a Vision-based Page Segmentation Algorithm
(2003)

A new web content structure analysis based on visual representation is proposed in this paper. Many web applications such as information retrieval, information extraction and automatic page adaptation can benefit from this structure. This paper presents an automatic top-down, tag-tree independent approach to detect web content structure. It simulates how a user understands web layout structure based on his visual perception. Comparing to other existing techniques, our approach is independent to underlying documentation representation such as HTML and works well even when the HTML structure is far different from layout structure. Experiments show satisfactory results.
Modality Effects in Deception Detection and Applications in Automatic-Deception-Detection
(2005)

Modality is an important context factor in deception, which is context-dependent. In order to build a reliable and flexible tool for automatic-deception-detection (ADD), we investigated the characteristics of verbal cues to deceptive behavior in three modalities: text, audio and face-to-face communication. Seven categories of verbal cues (21 cues) were studied: quantity, complexity, diversity, verb nonimmediacy, uncertainty, specificity and affect. After testing the interaction effects between modality and condition (deception or truth), we found significance only with specificity and observed that differences between deception and truth were in general consistent across the three modalities. However, modality had strong effects on verbal cues. For example, messages delivered face-to-face were largest in quantity (number of words, verbs, and sentences), followed by the audio modality. Text had the sparsest examples. These modality effects are an important factor in building baselines in ADD tools, because they make it possible to use them to adjust the baseline for an unknown modality according to a known baseline, thereby simplifying the process of ADD. The paper discusses in detail the implications of these findings on modality effects in three modalities.
Model-based clustering of high-dimensional data: A review
(2014)

Model-based clustering is a popular tool which is renowned for its probabilistic foundations and its flexibility. However, high-dimensional data are nowadays more and more frequent and, unfortunately, classical model-based clustering techniques show a disappointing behavior in high-dimensional spaces. This is mainly due to the fact that model-based clustering methods are dramatically over-parametrized in this case. However, high-dimensional spaces have specific characteristics which are useful for clustering and recent techniques exploit those characteristics. After having recalled the bases of model-based clustering, this article will review dimension reduction approaches, regularization-based techniques, parsimonious modeling, subspace clustering methods and clustering methods based on variable selection. Existing softwares for model-based clustering of high-dimensional data will be also reviewed and their practical use will be illustrated on real-world data sets.
Categorical Data Clustering using Frequency and Tf-Idf based Cosine Similarity
(2014)

Clustering is the process of grouping a set of physical objects into classes of similar object. Objects in real world consist of both numerical and categorical data. Categorical data are not analyzed as numerical data due to the lack of inherit ordering. This paper describes Frequency and Tf-Idf Based Categorical Data Clustering (FTCDC) technique based on cosine similarity measure. The FTCDC system consists of four modules, such as data pre-processing, similarity matrix generation, cluster formation and validation. The System architecture of FTCDC is explained and its performance is examined using a simple example scenario. The performance on real world data is measured using accuracy and error rate. The performance of the system much relay on the similarity threshold selected for the clustering process.
Transcription Methods for Consistency, Volume and Efficiency
(2010)

This paper describes recent efforts at Linguistic Data Consortium at the University of Pennsylvania to create manual transcripts as a shared resource for human language technology research and evaluation. Speech recognition and related technologies in particular call for substantial volumes of transcribed speech for use in system development, and for human gold standard references for evaluating performance over time. Over the past several years LDC has developed a number of transcription approaches to support the varied goals of speech technology evaluation programs in multiple languages and genres. We describe each transcription method in detail, and report on the results of a comparative analysis of transcriber consistency and efficiency, for two transcription methods in three languages and five genres. Our findings suggest that transcripts for planned speech are generally more consistent than those for spontaneous speech, and that careful transcription methods result in higher rates of agreement when compared to quick transcription methods. We conclude with a general discussion of factors contributing to transcription quality, efficiency and consistency.
GraphP: Reducing Communication for PIM-Based Graph Processing with Efficient Data Partition
(2018)

Processing-In-Memory (PIM) is an effective technique that reduces data movements by integrating processing units within memory. The recent advance of “big data” and 3D stacking technology make PIM a practical and viable solution for the modern data processing workloads. It is exemplified by the recent research interests on PIM-based acceleration. Among them, TESSERACT is a PIM-enabled parallel graph processing architecture based on Micron’s Hybrid Memory Cube (HMC), one of the most prominent 3D-stacked memory technologies. It implements a Pregel-like vertex-centric programming model, so that users could develop programs in the familiar interface while taking advantage of PIM. Despite the orders of magnitude speedup compared to DRAM-based systems, TESSERACT generates excessive crosscube communications through SerDes links, whose bandwidth is much less than the aggregated local bandwidth of HMCs. Our investigation indicates that this is because of the restricted data organization required by the vertex programming model. In this paper, we argue that a PIM-based graph processing system should take data organization as a first-order design consideration. Following this principle, we propose GraphP, a novel HMC-based software/hardware co-designed graph processing system that drastically reduces communication and energy consumption compared to TESSERACT. GraphP features three key techniques. 1) “Source-cut” partitioning, which fundamentally changes the cross-cube communication from one remote put per cross-cube edge to one update per replica. 2) “Two-phase Vertex Program”, a programming model designed for the “source-cut” partitioning with two operations: GenUpdate and ApplyUpdate. 3) Hierarchical communication and overlapping, which further improves performance with unique opportunities offered by the proposed partitioning and programming model. We evaluate GraphP using a cycle accurate simulator with 5 real-world graphs and 4 algorithms. The results show that it provides on average 1.7 speedup and 89% energy saving compared to TESSERACT.
Architectural optimizations for high performance and energy efficient Smith-Waterman implementation on FPGAs using OpenCL
(2017)

Smith-Waterman is a dynamic programming algorithm that plays a key role in the modern genomics pipeline as it is guaranteed to find the optimal local alignment between two strings of data. The state of the art presents many hardware acceleration solutions that have been implemented in order to exploit the high degree of parallelism available in this algorithm. The majority of these implementations use heuristics to increase the performance of the system at the expense of the accuracy of the result. In this work, we present an implementation of the pure version of the algorithm. We include the key architectural optimizations to achieve highest possible performance for a given platform and leverage the Berkeley roofline model to track the performance and guide the optimizations. To achieve scalability, our custom design comprises of systolic arrays, data compression features and shift registers, while a custom port mapping strategy aims to maximize performance. Our designs are built leveraging an OpenCL-based design entry, namely Xilinx SDAccel, in conjunction with a Xilinx Virtex 7 and Kintex Ultrascale platform. Our final design achieves a performance of 42.47 GCUPS (giga cell updates per second) with an energy efficiency of 1.6988 GCUPS/W. This represents an improvement of 1.72x in performance and energy efficiency over previously published FPGA implementations and 8.49x better in energy efficiency over comparable GPU implementations.
An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics
(2015)

MOTIVATION
The field of phylodynamics focuses on the problem of reconstructing population size dynamics over time using current genetic samples taken from the population of interest. This technique has been extensively used in many areas of biology but is particularly useful for studying the spread of quickly evolving infectious diseases agents, e.g. influenza virus. Phylodynamic inference uses a coalescent model that defines a probability density for the genealogy of randomly sampled individuals from the population. When we assume that such a genealogy is known, the coalescent model, equipped with a Gaussian process prior on population size trajectory, allows for nonparametric Bayesian estimation of population size dynamics. Although this approach is quite powerful, large datasets collected during infectious disease surveillance challenge the state-of-the-art of Bayesian phylodynamics and demand inferential methods with relatively low computational cost.


RESULTS
To satisfy this demand, we provide a computationally efficient Bayesian inference framework based on Hamiltonian Monte Carlo for coalescent process models. Moreover, we show that by splitting the Hamiltonian function, we can further improve the efficiency of this approach. Using several simulated and real datasets, we show that our method provides accurate estimates of population size dynamics and is substantially faster than alternative methods based on elliptical slice sampler and Metropolis-adjusted Langevin algorithm.


AVAILABILITY AND IMPLEMENTATION
The R code for all simulation studies and real data analysis conducted in this article are publicly available at http://www.ics.uci.edu/∼slan/lanzi/CODES.html and in the R package phylodyn available at https://github.com/mdkarcher/phylodyn.


CONTACT
S.Lan@warwick.ac.uk or babaks@uci.edu


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Multiuser Millimeter Wave Communications With Nonorthogonal Beams
(2017)

Recently, millimeter-wave (mmWave) and even terahertz wireless (with higher frequency) networks have attracted significant research interests as alternatives to support the formidable growth of wireless communication services. Normally, directional beamforming (BF) is shown as a promising technique to compensate its high path loss. We focus on mmWave communications and assume that both mmWave base stations (MBSs) and user equipments (UEs) can support directional BF. As mmWave spectrum has short wavelength, massive antenna arrays can be deployed at MBSs to form multiple directional beams through BF training. Then, an MBS can transmit simultaneously to multiple UEs (SUEs) with different beams in the networks. However, the beams that serve different SUEs may transmit (almost) in the same path, especially when SUEs are distributed densely. Thus, they are not in perfect orthogonal beams. Due to the leakage of transmission power, the interference among these beams may be severe. To address this problem, typically the MBS could serve these SUEs in time division multiplex. This will degrade the spectral efficiency. In this context, we investigate the effect of nonorthogonal beam interference and then propose two novel solutions (i.e., dynamic beam switching and static beam selection) to coordinate the transmitting beams effectively. Then, an improved downlink multiuser simultaneous transmission scheme is introduced. In the scheme, an MBS can serve multiple SUEs simultaneously with multiple orthogonal and/or nonorthogonal beams to guarantee SUEs’ Quality of Service. The theoretical and numerical results have shown that our scheme can largely improve the performance of the achievable rate and, meanwhile, can serve lots of SUEs simultaneously.
An Adaptive Privacy Protection Method for Smart Home Environments Using Supervised Learning
(2017)

In recent years, smart home technologies have started to be widely used, bringing a great deal of convenience to people’s daily lives. At the same time, privacy issues have become particularly prominent. Traditional encryption methods can no longer meet the needs of privacy protection in smart home applications, since attacks can be launched even without the need for access to the cipher. Rather, attacks can be successfully realized through analyzing the frequency of radio signals, as well as the timestamp series, so that the daily activities of the residents in the smart home can be learnt. Such types of attacks can achieve a very high success rate, making them a great threat to users’ privacy. In this paper, we propose an adaptive method based on sample data analysis and supervised learning (SDASL), to hide the patterns of daily routines of residents that would adapt to dynamically changing network loads. Compared to some existing solutions, our proposed method exhibits advantages such as low energy consumption, low latency, strong adaptability, and effective privacy protection.
65GHz Doppler Sensor with On-Chip Antenna in 0.18μm SiGe BiCMOS
(2006)

A single-chip 65GHz Doppler radar transceiver with on-chip patch antenna is reported. Implemented in a production 0.18mum SiGe BiCMOS process, it features a differential output transmit power of 4.3dBm, 16.5dB single-ended down-conversion gain and a double-sideband noise figure of 12.8dB. The radar includes a 65GHz 2-stage cascode LNA with S 11<-15dB at 50-94GHz and 14dB gain at 65GHz, a double-balanced down-convert mixer, a SiGe HBT IF amplifier with low 1/f noise, a VCO and a 65GHz output buffer. The LO is provided by an integrated varactor-tuned 61-67GHz VCO optimized for low phase noise. The patch antenna is designed to be impedance-matched for dual-band operation at 62.8 and 64.6GHz. The use of lumped inductors in all blocks and a vertically-stacked transformer for single-ended to differential conversion in the receive path help reduce the transceiver area to 1mm times 1mm
In-class distractions: The role of Facebook and the primary learning task
(2016)

While laptops and other Internet accessible technologies facilitate student learning in the classroom, they also increase opportunities for interruptions from off-task social networking sites such as Facebook (FB). A small number of correlational studies have suggested that FB has a detrimental effect on learning performance, however; these studies had neglected to investigate student-engagement in the primary learning task and how this affects task-switching to goal-irrelevant FB intrusions (distractions); and how purposeful deployment of attention to FB (goal-relevant interruptions) affect lecture comprehension on such tasks. This experiment fills a gap in the literature by manipulating lecture interest-value and controls for duration of FB exposure, time of interruption, FB material and the order of FB posts. One hundred and fifty participants were randomly allocated to one of six conditions: (A) no FB intrusions, high-interest (HI) lecture; (B) no FB intrusions, low-interest (LI) lecture (C) goal-relevant FB intrusions, HI lecture (D) goal-relevant FB intrusions, LI lecture (E) goal-irrelevant FB intrusions, HI lecture (F) goal-irrelevant FB intrusions, LI lecture. As predicted, participants were more susceptible to FB distractions when the primary learning task was of low-interest. The study also found that goal-relevant FB intrusions significantly reduced HI lecture comprehension compared to the control condition (A). The results highlight the need for recourses that will help educators increase student engagement with their learning task. Implications for future research are discussed. 2014 Elsevier Ltd. All rights reserved.